Formate-nitrite transporter

Form_Nir_trans
Identifiers
SymbolForm_Nir_trans
PfamPF01226
InterProIPR000292
PROSITEPDOC00769
TCDB2.A.44
OPM superfamily7
OPM protein3tdp
Available protein structures:
Pfam  structures / ECOD  
PDBRCSB PDB; PDBe; PDBj
PDBsumstructure summary

The Formate-Nitrite Transporter (FNT) Family belongs to the Major Intrinsic Protein (MIP) Superfamily.[1][2] FNT family members have been sequenced from Gram-negative and Gram-positive bacteria, archaea, yeast, plants and lower eukaryotes. The prokaryotic proteins of the FNT family probably function in the transport of the structurally related compounds, formate and nitrite.[3]

Structure

With the exception of the yeast protein (627 amino acyl residues), all characterized members of the family are of 256-285 residues in length and exhibit 6-8 putative transmembrane α-helical spanners (TMSs). In one case, that of the E. coli FocA (TC# 1.A.16.1.1) protein, a 6 TMS topology has been established.[4] The yeast protein has a similar apparent topology but has a large C-terminal hydrophilic extension of about 400 residues.

FocA of E. coli is a symmetric pentamer, with each subunit consisting of six TMSs.[4]

Phylogeny

The phylogenetic tree shows clustering according to function and organismal phylogeny. The putative formate efflux transporters (FocA; TC#s 1.A.16.1.1 and 1.A.16.1.3) of bacteria associated with pyruvate-formate lyase (pfl) comprise cluster I; the putative formate uptake permeases (FdhC; TC#s 1.A.16.2.1 and 1.A.16.2.3) of bacteria and archaea associated with formate dehydrogenase comprise cluster II; the nitrite uptake permeases (NirC, TC#s 1.A.16.2.5, 1.A.16.3.1, and 1.A.16.3.4) of bacteria comprise cluster III, and a yeast protein comprises cluster IV.[5]

Function

The energy coupling mechanisms for proteins of the FNT family have not been extensively characterized. HCO−
2 and NO−
2 uptakes may be coupled to H+ symport. HCO−
2 efflux may be driven by the membrane potential by a uniport mechanism or by H+ antiport. FocA of E. coli catalyzes bidirectional formate transport and may function by a channel-type mechanism.[6]

FocA, transports short-chain acids. FocA may be able to switch its mode of operation from a passive export channel at high external pH to a secondary active formate/H+ importer at low pH. The crystal structure of Salmonella typhimurium FocA at pH 4.0 shows that this switch involves a major rearrangement of the amino termini of individual protomers in the pentameric channel.[7] The amino-terminal helices open or block transport in a concerted, cooperative action that indicates how FocA is gated in a pH-dependent way. Electrophysiological studies show that the protein acts as a specific formate channel at pH 7.0 and that it closes upon a shift of pH to 5.1.

Transport Reaction

The probable transport reactions catalyzed by different members of the FNT family are:

(1) RCO−
2 or NO−
2 (out) ⇌ RCO−
2 or NO−
2 (in),

(2) HCO−
2 (in) ⇌ HCO−
2 (out),

(3) HS− (out) ⇌ HS− (in).

Members

A representative list of the currently classified members belonging to the FNT family can be found in the Transporter Classification Database. Some characterized members include:

  • FocA and FocB (TC#s 1.A.16.1.1 and 1.A.16.1.2, respectively), from Escherichia coli, transporters involved in the bidirectional transport of formate.
  • FdhC, from Methanobacterium maripaludis (TC# 1.A.16.2.3) and Methanothermobacter thermoformicicum (TC# 1.A.16.2.1), a probable formate transporter.
  • NirC, from E. coli (TC# 1.A.16.3.1), a probable nitrite transporter.
  • Nar1 (TC# 1.A.16.2.4) of Chlamydomonas reinhardtii (Chlamydomonas smithii), a nitrite uptake porter of 355 amino acyl residues.
  • B. subtilis hypothetical protein YwcJ (ipa-48R) (TC# 1.A.16.3.2).

References

  1. ^ Reizer J, Reizer A, Saier MH (1993-01-01). "The MIP family of integral membrane channel proteins: sequence comparisons, evolutionary relationships, reconstructed pathway of evolution, and proposed functional differentiation of the two repeated halves of the proteins". Critical Reviews in Biochemistry and Molecular Biology. 28 (3): 235–57. doi:10.3109/10409239309086796. PMID 8325040.
  2. ^ Park JH, Saier MH (October 1996). "Phylogenetic characterization of the MIP family of transmembrane channel proteins". The Journal of Membrane Biology. 153 (3): 171–80. doi:10.1007/s002329900120. PMID 8849412. S2CID 1559932.
  3. ^ Suppmann B, Sawers G (March 1994). "Isolation and characterization of hypophosphite--resistant mutants of Escherichia coli: identification of the FocA protein, encoded by the pfl operon, as a putative formate transporter". Molecular Microbiology. 11 (5): 965–82. doi:10.1111/j.1365-2958.1994.tb00375.x. PMID 8022272. S2CID 6425651.
  4. ^ a b Wang Y, Huang Y, Wang J, Cheng C, Huang W, Lu P, Xu YN, Wang P, Yan N, Shi Y (November 2009). "Structure of the formate transporter FocA reveals a pentameric aquaporin-like channel". Nature. 462 (7272): 467–72. Bibcode:2009Natur.462..467W. doi:10.1038/nature08610. PMID 19940917. S2CID 4370839.
  5. ^ Saier, MH Jr. "1.A.16 The Formate-Nitrite Transporter (FNT) Family". Transporter Classification Database. Saier Lab Bioinformatics Group / SDSC.
  6. ^ Falke D, Schulz K, Doberenz C, Beyer L, Lilie H, Thiemer B, Sawers RG (February 2010). "Unexpected oligomeric structure of the FocA formate channel of Escherichia coli : a paradigm for the formate-nitrite transporter family of integral membrane proteins". FEMS Microbiology Letters. 303 (1): 69–75. doi:10.1111/j.1574-6968.2009.01862.x. PMID 20041954.
  7. ^ Lü W, Du J, Wacker T, Gerbig-Smentek E, Andrade SL, Einsle O (April 2011). "pH-dependent gating in a FocA formate channel". Science. 332 (6027): 352–4. Bibcode:2011Sci...332..352L. doi:10.1126/science.1199098. PMID 21493860. S2CID 20059830.
This article incorporates text from the public domain Pfam and InterPro: IPR000292